Nathan:
I'm not a PE, but I do generally understand safety factors and caution in engineering.
However, presuming that the repairs/replacements of the segments do occur as described in the report, how would the bridge be any weaker than it has been for the last 120+ years?
K-36's and K-37's have been trundling across this bridge since the 1920's with the same or heavier loading than today's trains. 80+ years of K series locomotives have crossed Lobato. Roughly an average of at least two locomotives per day, probably 3 to 5 per day before 1968 due to Cumbres Turns -- say, a minimum of 25,000 crossings, perhaps as many as 100,000 (?) without bridge failures. Your scenario of pounding has to have happened a bunch of times in that period. I don't have any number for how much extra load that pounding might apply, but the historical evidence says that it isn't enough to cause a failure.
If didn't cause *any* failures at Lobato, why would we expect the newly repaired structure to have a catastrophic failure? Murphy's Law always applies, but I think Murphy might be tired of watching Lobato by now :-)